/*
* Copyright 2019-2020 NVIDIA CORPORATION.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*     http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/

#pragma once

#include "matrix_cpu.hpp"

#include <vector>
#include <string>

namespace claraparabricks
{

namespace genomeworks
{

namespace cudaaligner
{

matrix<int> needleman_wunsch_build_score_matrix_naive(std::string const& text, std::string const& query);

std::vector<int8_t> needleman_wunsch_cpu(std::string const& text, std::string const& query);

} // namespace cudaaligner

} // namespace genomeworks

} // namespace claraparabricks
